tophat2 mapping fr-firststrand or fr-secondstrand ?

Question

[debitboro]

Dear all,

I've paired-end sequencing reads generated by a strand-specific library (AB SOLiD System), I'm trying to map them to a reference transcriptome using tophat2 and using either --library-type fr-firststrand or --library-type fr-secondtstrand arguments, but I got the same results for both cases !!!

The result of mapping:

      Left reads:
      Input     :     82874
       Mapped   :     60895 (73.5% of input)
        of these:      1821 ( 3.0%) have multiple alignments (24 have >20)
      Right reads:
      Input     :     82874
       Mapped   :     67550 (81.5% of input)
        of these:      2053 ( 3.0%) have multiple alignments (23 have >20)
      77.5% overall read mapping rate.

      Aligned pairs:     55845
             of these:      1646 ( 2.9%) have multiple alignments
                 200 ( 0.4%) are discordant alignments
      67.1% concordant pair alignment rate.

BTW, before mapping I've checked the strandness of the library using the infer_experiment.py script from the package RSeQC, and the result seemed the library is strand-specific.

Thank you in advance